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comparison galaxy_stubs/IMGDock.xml @ 2:605370bc1def draft default tip

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author luis
date Tue, 12 Jul 2016 12:33:33 -0400
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1:31013b5cd066 2:605370bc1def
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Docking]-->
4 <tool id="IMGDock" name="IMGDock" version="1.1.0">
5 <description>Iterative Multi-Greedy Docking</description>
6 <macros>
7 <token name="@EXECUTABLE@">IMGDock</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>IMGDock
13
14 #if $param_rec:
15 -rec $param_rec
16 #end if
17 #if $param_rl:
18 -rl $param_rl
19 #end if
20 #if $param_pocket:
21 -pocket $param_pocket
22 #end if
23 #if $param_i:
24 -i $param_i
25 #end if
26 #if $param_o:
27 -o $param_o
28 #end if
29 #if $param_grd:
30 -grd $param_grd
31 #end if
32 #if $param_rm:
33 -rm $param_rm
34 #end if
35 #if $adv_opts.adv_opts_selector=='advanced':
36 #if $adv_opts.param_IMGDock_superpose_ligand:
37 -IMGDock:superpose_ligand
38 #end if
39 #if $adv_opts.param_IMGDock_decrease_stepwidth:
40 -IMGDock:decrease_stepwidth
41 #end if
42 #if $adv_opts.param_IMGDock_output_failed_dockings:
43 -IMGDock:output_failed_dockings
44 #end if
45 #if $adv_opts.param_IMGDock_iterations:
46 -IMGDock:iterations $adv_opts.param_IMGDock_iterations
47 #end if
48 #if $adv_opts.param_IMGDock_min_inhibitor_atoms:
49 -IMGDock:min_inhibitor_atoms $adv_opts.param_IMGDock_min_inhibitor_atoms
50 #end if
51 #if $adv_opts.param_IMGDock_post_optimization_step_width:
52 -IMGDock:post_optimization_step_width $adv_opts.param_IMGDock_post_optimization_step_width
53 #end if
54 #if $adv_opts.param_IMGDock_no_solutions:
55 -IMGDock:no_solutions $adv_opts.param_IMGDock_no_solutions
56 #end if
57 #if $adv_opts.param_IMGDock_post_optimization_steps:
58 -IMGDock:post_optimization_steps $adv_opts.param_IMGDock_post_optimization_steps
59 #end if
60 #if $adv_opts.param_IMGDock_step_width:
61 -IMGDock:step_width $adv_opts.param_IMGDock_step_width
62 #end if
63 #if $adv_opts.param_ScoringFunction_filename:
64 -ScoringFunction:filename $adv_opts.param_ScoringFunction_filename
65 #end if
66 #if $adv_opts.param_ScoringFunction_electrostatic_cuton:
67 -ScoringFunction:electrostatic_cuton $adv_opts.param_ScoringFunction_electrostatic_cuton
68 #end if
69 #if $adv_opts.param_ScoringFunction_electrostatic_cutoff:
70 -ScoringFunction:electrostatic_cutoff $adv_opts.param_ScoringFunction_electrostatic_cutoff
71 #end if
72 #if $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap:
73 -ScoringFunction:allowed_intermolecular_overlap $adv_opts.param_ScoringFunction_allowed_intermolecular_overlap
74 #end if
75 #if $adv_opts.param_ScoringFunction_ignore_H_clashes:
76 -ScoringFunction:ignore_H_clashes
77 #end if
78 #if $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap:
79 -ScoringFunction:allowed_intramolecular_overlap $adv_opts.param_ScoringFunction_allowed_intramolecular_overlap
80 #end if
81 #if $adv_opts.param_ScoringFunction_burial_depth_scale:
82 -ScoringFunction:burial_depth_scale $adv_opts.param_ScoringFunction_burial_depth_scale
83 #end if
84 #if $adv_opts.param_ScoringFunction_vdw_cutoff:
85 -ScoringFunction:vdw_cutoff $adv_opts.param_ScoringFunction_vdw_cutoff
86 #end if
87 #if $adv_opts.param_ScoringFunction_nonbonded_cutoff:
88 -ScoringFunction:nonbonded_cutoff $adv_opts.param_ScoringFunction_nonbonded_cutoff
89 #end if
90 #if $adv_opts.param_ScoringFunction_hashgrid_size:
91 -ScoringFunction:hashgrid_size $adv_opts.param_ScoringFunction_hashgrid_size
92 #end if
93 #if $adv_opts.param_ScoringFunction_vdw_cuton:
94 -ScoringFunction:vdw_cuton $adv_opts.param_ScoringFunction_vdw_cuton
95 #end if
96 #if $adv_opts.param_ScoringFunction_hashgrid_resolution:
97 -ScoringFunction:hashgrid_resolution $adv_opts.param_ScoringFunction_hashgrid_resolution
98 #end if
99 #end if
100 </command>
101 <inputs>
102 <param name="param_rec" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="receptor pdb-file" help="(-rec) "/>
103 <param name="param_rl" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="reference-ligand" help="(-rl) "/>
104 <param name="param_pocket" type="data" format="ini" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="configuration file" help="(-pocket) "/>
105 <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="compounds to be docked" help="(-i) "/>
106 <param name="param_grd" type="data" format="bngrd,grd,grd.gz,bngrd.gz" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="ScoreGrid file" help="(-grd) "/>
107 <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/>
108 <expand macro="advanced_options">
109 <param name="param_IMGDock_superpose_ligand" type="boolean" truevalue="-IMGDock:superpose_ligand" falsevalue="" checked="true" optional="True" label="superpose ligands with ref.-ligand" help="(-superpose_ligand) "/>
110 <param name="param_IMGDock_decrease_stepwidth" type="boolean" truevalue="-IMGDock:decrease_stepwidth" falsevalue="" checked="false" optional="True" label="decrease step-width in each iterations" help="(-decrease_stepwidth) "/>
111 <param name="param_IMGDock_output_failed_dockings" type="boolean" truevalue="-IMGDock:output_failed_dockings" falsevalue="" checked="false" optional="True" label="output erroneous molecules" help="(-output_failed_dockings) "/>
112 <param name="param_IMGDock_iterations" type="integer" min="1" max="20" optional="True" value="4" label="max. IMG iterations" help="(-iterations) "/>
113 <param name="param_IMGDock_min_inhibitor_atoms" type="integer" min="0" max="100" optional="True" value="10" label="min. atoms in ref. lig. area" help="(-min_inhibitor_atoms) "/>
114 <param name="param_IMGDock_post_optimization_step_width" type="float" min="0.1" max="2.0" optional="True" value="0.5" label="translation opt. step-width" help="(-post_optimization_step_width) "/>
115 <param name="param_IMGDock_no_solutions" type="integer" min="10" max="1000" optional="True" value="100" label="num. multi-greedy solutions" help="(-no_solutions) "/>
116 <param name="param_IMGDock_post_optimization_steps" type="integer" min="0" max="10" optional="True" value="6" label="max. translation opt. steps" help="(-post_optimization_steps) "/>
117 <param name="param_IMGDock_step_width" type="integer" min="1" max="90" optional="True" value="10" label="step-width (bond angle discretization)" help="(-step_width) "/>
118 <param name="param_ScoringFunction_filename" type="data" format="ini" optional="True" value="Amber/amber96-docking.ini" label="file with electrostatics and vdW parameters" help="(-filename) "/>
119 <param name="param_ScoringFunction_electrostatic_cuton" type="float" value="17.0" label="electrostatic cuton" help="(-electrostatic_cuton) "/>
120 <param name="param_ScoringFunction_electrostatic_cutoff" type="float" value="20.0" label="electrostatic cutoff" help="(-electrostatic_cutoff) "/>
121 <param name="param_ScoringFunction_allowed_intermolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intermolecular atom-overlap" help="(-allowed_intermolecular_overlap) "/>
122 <param name="param_ScoringFunction_ignore_H_clashes" type="boolean" truevalue="-ScoringFunction:ignore_H_clashes" falsevalue="" checked="true" optional="True" label="ignore clashes involving hydrogens" help="(-ignore_H_clashes) "/>
123 <param name="param_ScoringFunction_allowed_intramolecular_overlap" type="float" min="0.0" max="2.0" optional="True" value="1.0" label="allowed intramolecular atom-overlap" help="(-allowed_intramolecular_overlap) "/>
124 <param name="param_ScoringFunction_burial_depth_scale" type="float" min="1.0" max="5.0" optional="True" value="1.0" label="relative-depth-of-burial scale" help="(-burial_depth_scale) "/>
125 <param name="param_ScoringFunction_vdw_cutoff" type="float" value="20.0" label="vdw cutoff" help="(-vdw_cutoff) "/>
126 <param name="param_ScoringFunction_nonbonded_cutoff" type="float" value="20.0" label="nonbonded cutoff" help="(-nonbonded_cutoff) "/>
127 <param name="param_ScoringFunction_hashgrid_size" type="integer" value="10" label="hashgrid size (num of boxes)" help="(-hashgrid_size) "/>
128 <param name="param_ScoringFunction_vdw_cuton" type="float" value="17.0" label="vdw cuton" help="(-vdw_cuton) "/>
129 <param name="param_ScoringFunction_hashgrid_resolution" type="integer" min="1" max="5" optional="True" value="3" label="hashgrid resolution" help="(-hashgrid_resolution) "/>
130 </expand>
131 </inputs>
132 <outputs>
133 <data name="param_o" format="mol2"/>
134 </outputs>
135 <help>IMGDock docks compounds into the binding pocket of a receptor using an iterative multi-greedy approach.
136 As input we need:
137
138 * a file containing a protonated protein in pdb-format
139 * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
140 * a score-grid file generated by GridBuilder. This grid must have been precalculated for the same receptor and reference ligand as those that are to be used here.
141 * a file containing the compounds that are to be docked. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). These molecules must have been assigned 3D coordinates (e.g. by Ligand3DGenerator) and should have been checked for errors using LigCheck.
142
143 Output of this tool is a file containing all compounds docked into the binding pocket, with a property-tag named 'score' indicating the score obtained for each compound.
144
145 Tip: If you want to parallelize docking, use LigandFileSplitter to separate your input file containing the compounds to be docked into several batches, dock each batch with this tool and merge the output files with DockResultMerger.
146
147 </help>
148 </tool>